Dynamic documents with R and knitr

Machine generated contents note: 2.1.Literature

2.2.Good and Bad Practices

2.3.Barriers

3.1.Setup

3.2.Minimal Examples

3.2.1.An Example in LATEX

3.2.2.An Example in Markdown

3.3.Quick Reporting

3.4.Extracting R Code

4.1.RStudio

4.2.LYX

4.3.Emacs/ESS

4.4.Other Editors

5.1.Input Syntax

5.1.1.Chunk Options

5.1.2.Chunk Label

5.1.3.Global Options

5.1.4.Chunk Syntax

5.2.Document Formats

5.2.1.Markdown

5.2.2.LATEX

5.2.3.HTML

5.2.4.reStructuredText

5.2.5.Customization

5.3.Output Renderers

5.4.R Scripts

6.1.Inline Output

6.2.Chunk Output

6.2.1.Chunk Evaluation

6.2.2.Code Formatting

6.2.3.Code Decoration

6.2.4.Show/Hide Output

6.3.Tables

6.4.Themes

7.1.Graphical Devices

7.1.1.Custom Device

7.1.2.Choose a Device

7.1.3.Device Size

7.1.4.More Device Options

7.1.5.Encoding

7.1.6.The Dingbats Font

7.2.Plot Recording

7.3.Plot Rearrangement

7.3.1.Animation

7.3.2.Alignment

7.4.Plot Size in Output

7.5.Extra Output Options

7.6.The tikz Device

7.7.Figure Environment

7.8.Figure Path

8.1.Implementation

8.2.Write Cache

8.3.When to Update Cache

8.4.Side Effects

8.5.Chunk Dependencies

8.5.1.Manual Dependency

8.5.2.Automatic Dependency

9.1.Chunk Reference

9.1.1.Embed Code Chunks

9.1.2.Reuse Whole Chunks

9.2.Code Externalization

9.2.1.Labeled Chunks

9.2.2.Line-based Chunks

9.3.Child Documents

9.3.1.Input Child Documents

9.3.2.Child Documents as Templates

9.3.3.Standalone Mode

10.1.Chunk Hooks

10.1.1.Create Chunk Hooks

10.1.2.Trigger Chunk Hooks

10.1.3.Hook Arguments

10.1.4.Hooks and Chunk Options

10.1.5.Write Output

10.2.Examples

10.2.1.Crop Plots

10.2.2.rgl Plots

10.2.3.Manually Save Plots

10.2.4.Optimize PNG Plots

10.2.5.Close an rgl Device

10.2.6.WebGL

11.1.Design

11.1.1.The Engine Function

11.1.2.Engine Options

11.2.Languages and Tools

11.2.1.C++

11.2.2.Interpreted Languages

11.2.3.TikZ

11.2.4.Graphviz

11.2.5.Highlight

12.1.Chunk Options

12.1.1.Option Aliases

12.1.2.Option Templates

12.1.3.Program Chunk Options

12.1.4.Code in Appendix

12.2.Package Options

12.3.Typesetting

12.3.1.Output Width

12.3.2.Message Colors

12.3.3.Box Padding

12.3.4.Beamer

12.3.5.Suppress Long Output

12.3.6.Escape Special Characters

12.3.7.The Example Environment

12.4.Utilities

12.4.1.R Package Citation

12.4.2.Image URI

12.4.3.Upload Images

12.4.4.Compile Documents

12.4.5.Construct Code Chunks

12.4.6.Extract Source Code

12.4.7.Reproducible Simulation

12.4.8.R Documentation

12.4.9.Rst2pdf

12.4.10.Package Demos

12.4.11.Pretty Printing

12.4.12.A Macro Preprocessor

12.5.Debugging

12.6.Multilingual Support

13.1.RStudio

13.2.Pandoc

13.3.HTML5 Slides

13.4.Jekyll

13.5.WordPress

14.1.Homework

14.2.Web Site and Blogging

14.2.1.Vistat and Rcpp Gallery

14.2.2.UCLA R Tutorial

14.2.3.The cda and RHadoop Wiki

14.2.4.The ggbio Package

14.2.5.Geospatial Data in R and Beyond

14.3.Package Vignettes

14.3.1.PDF Vignette

14.3.2.HTML Vignette

14.4.Books

14.4.1.This Book

14.4.2.The Analysis of Data

14.4.3.The Statistical Sleuth in R

15.1.Sweave

15.1.1.Syntax

15.1.2.Options

15.1.3.Problems

15.2.Other R Packages

15.3.Python Packages

15.3.1.Dexy

15.3.2.Python TEX

15.3.3.IPython

15.4.More Tools

15.4.1.Org-mode

15.4.2.SASweave

15.4.3.Office

A.1.Documentation

A.2.Closures

A.3.Implementation

A.3.1.Parser

A.3.2.Chunk Hooks

A.3.3.Option Aliases

A.3.4.Cache

A.3.5.Compatibility with Sweave

A.3.6.Concordance

A.4.Syntax.